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'''STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS''' | '''STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS''' | ||
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==About this Structure== | ==About this Structure== | ||
2APR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhizopus_microsporus_var._chinensis Rhizopus microsporus var. chinensis]. This structure supersedes the now removed PDB entry | 2APR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhizopus_microsporus_var._chinensis Rhizopus microsporus var. chinensis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1apr 1apr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2APR OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Davies, D R.]] | [[Category: Davies, D R.]] | ||
[[Category: Suguna, K.]] | [[Category: Suguna, K.]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:19:33 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 19:19, 3 May 2008
STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS
OverviewOverview
The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 A, and for angle distances it is 0.034 A. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile "flap", a beta-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.
About this StructureAbout this Structure
2APR is a Single protein structure of sequence from Rhizopus microsporus var. chinensis. This structure supersedes the now removed PDB entry 1apr. Full crystallographic information is available from OCA.
ReferenceReference
Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis., Suguna K, Bott RR, Padlan EA, Subramanian E, Sheriff S, Cohen GH, Davies DR, J Mol Biol. 1987 Aug 20;196(4):877-900. PMID:3316666 Page seeded by OCA on Sat May 3 19:19:33 2008